66 commits

Author	SHA1	Message	Date
Maxime Garcia	ea6fde0193	Merge pull request #252 from MaxUlysse/master_tiddit ... New module: tiddit	2021-02-25 09:34:33 +01:00
MaxUlysse	f62196a4a6	feat: add tiddit_sv module	2021-02-24 15:59:10 +01:00
Harshil Patel	50b98d56a1	Merge pull request #246 from drpatelh/master ... Update iVar modules	2021-02-24 13:00:05 +00:00
Harshil Patel	5287fe5f95	Merge pull request #245 from phue/bismark_deduplicate ... add bismark/deduplicate + tests	2021-02-23 21:08:24 +00:00
Harshil Patel	4703a60443	Merge pull request #220 from phue/bwameth ... add bwameth modules	2021-02-23 21:01:54 +00:00
drpatelh	aaaef7df8c	Add BAM index	2021-02-23 20:42:16 +00:00
phue	e73bda26f5	add bismark/deduplicate + tests	2021-02-23 18:02:16 +01:00
kevinmenden	43446bc37e	added sarscov2 fastq and bam files	2021-02-22 13:19:12 +01:00
kevinmenden	bb5c0ceca5	adding SplitNCigarReads	2021-02-19 14:59:29 +01:00
Kevin Menden	0202162b17	Merge branch 'master' into gatk4-mergevcfs	2021-02-19 14:11:30 +01:00
kevinmenden	02abe106ec	added optional reference dictionary as input	2021-02-19 14:09:32 +01:00
kevinmenden	6dcaf5ffc8	add gatk4 bedtointervallist	2021-02-19 11:26:31 +01:00
phue	a963c67481	bwameth: pass genome index as directory ... instead of single files	2021-02-18 11:51:36 +01:00
Harshil Patel	5695e4ccce	Merge pull request #222 from phue/methyldackel ... add methyldackel modules	2021-02-17 22:17:26 +00:00
phue	5ad7c6bc51	add methyldackel/extract + tests + testdata	2021-02-17 19:18:55 +01:00
phue	84a5da0d91	add bwameth/align module + tests	2021-02-17 18:23:11 +01:00
Michael L Heuer	206b605666	Add module for seqwish/induce	2021-02-17 11:19:47 -06:00
Harshil Patel	a282ecd8c7	Merge pull request #172 from andersgs/ivar-variant ... Add ivar variants	2021-02-16 23:20:30 +00:00
MaxUlysse	fa34f806d2	chores: add bgzip files for tests	2021-02-16 17:06:09 +01:00
Anders Goncalves da Silva	89f65e0875	Merge branch 'master' into ivar-variant	2021-02-15 20:50:35 -08:00
Harshil Patel	8eb3acc43f	Merge pull request #171 from JoseEspinosa/mosdepth ... Add mosdepth module	2021-02-15 23:13:01 +00:00
Anders Goncalves da Silva	4af7414419	Add tests for ivar variants	2021-02-15 09:29:40 -08:00
JoseEspinosa	6e92a6a080	Adding mosdepth module	2021-02-15 14:33:44 +01:00
Maxime Garcia	ec0bf0145e	Merge branch 'master' into master_bwa-mem2	2021-02-15 13:08:52 +01:00
Anders Goncalves da Silva	6dca7799e6	Add ivar trim	2021-02-12 16:02:10 -08:00
Harshil Patel	63a20e7b5c	Merge pull request #168 from JoseEspinosa/bcftools_merge ... Add bcftools merge module	2021-02-12 23:20:30 +00:00
JoseEspinosa	5313698705	Add bcftools merge module	2021-02-13 00:08:57 +01:00
Anders Goncalves da Silva	0a6e8400ac	Add reference SC2 genome to test data	2021-02-12 11:27:12 -08:00
MaxUlysse	0afddf6ca4	fix: CI is working	2021-02-12 15:24:09 +01:00
Anders Goncalves da Silva	8f546a1f95	Add ivar consensus	2021-02-09 10:26:35 -08:00
JoseEspinosa	c93e96101a	Add untar module	2021-02-09 11:50:32 +01:00
Harshil Patel	84cf5ea2ef	Merge pull request #153 from JoseEspinosa/bedtools_maskfasta ... Add bedtools maskfasta module	2021-02-08 23:11:00 +00:00
Harshil Patel	132dabbbb6	Update tests/data/bed/C.bed	2021-02-08 23:03:26 +00:00
JoseEspinosa	02d10c25a3	Add bedtools maskfasta module	2021-02-08 23:41:10 +01:00
JoseEspinosa	4fa38ebb7a	Separate test data to break dependencies between bcftools modules tests	2021-02-08 16:51:21 +01:00
JoseEspinosa	5071bf5914	Merge remote-tracking branch 'upstream/master' into bcftools_viralrecon	2021-02-08 10:45:57 +01:00
Michael L Heuer	c466255f6f	Add bandage image module	2021-02-03 19:31:58 -06:00
JoseEspinosa	382ea31e7e	Adding bcftools test data	2021-02-02 09:18:28 +01:00
Harshil Patel	2c962f34df	Merge pull request #110 from luslab/master ... Add SEACR module containing a single CALLPEAK process	2021-02-01 09:48:15 +00:00
Harshil Patel	bd59706d51	Merge pull request #118 from heuermh/dsh-bio ... Added dsh-bio filter-bed as dsh_filterbed	2021-01-29 18:15:24 +00:00
kevinmenden	9156becd19	changed 'covid' to 'sarscov2'	2021-01-29 12:45:21 +01:00
kevinmenden	8d4b71355e	added test data and salmon tests	2021-01-26 15:24:06 +01:00
kevinmenden	f58c1c1e9e	added star genomegenerate test	2021-01-22 14:01:59 +01:00
Michael L Heuer	eb6408f3dc	Added dsh-bio filter-bed as dsh_filterbed	2021-01-21 15:16:20 -06:00
sruthipsuresh	7729fee5a9	Added gffread and gff3 file for testing	2021-01-15 10:32:20 -06:00
sruthipsuresh	7c88cf4f67	Finished module with md5sums	2021-01-12 09:29:31 -06:00
Chris Cheshire	4e55bdcf84	seacr | removed test files	2020-12-17 14:20:02 +00:00
Chris Cheshire	a964d98d7f	seacr | Added test data	2020-12-17 13:55:58 +00:00
Abhinav Sharma	5949bfc15b	Edit the location of multiqc_config file	2020-12-04 22:55:15 +05:30
Abhinav Sharma	27b4b29976	Remove the extra data files	2020-12-04 20:20:59 +05:30